Publications

If you are publishing figures or analyses made with RNAvigate, I would appreciate a citation! I will add your paper to this list.

RNAvigate: Efficient exploration of RNA chemical probing datasets

Papers that use RNAvigate in their analyses and figures

  1. Bair,C.R., VanInsberghe,D., Lowen,A.C., Conn,G.L. and Neufeldt,C.J. (2026) Comparative analysis of flavivirus sfRNA dynamics and secondary structure. 10.64898/2026.04.07.716965.

  2. Ehrhardt,J.E., Qiu,D.Y., Jin,S., Boerneke,M.A., Aufgebauer,C.J., Horner,S.M. and Weeks,K.M. (2025) A Small Cationic Probe for Accurate, Punctate Discovery of RNA Tertiary Structure. JACS Au, 5, 6287–6297.

  3. Allen,S.R., Schlick,T. and Laederach,A. (2025) RNA Structural Ensemble Determinants of −1 Programmed Ribosomal Frameshifting Efficiency Across Coronavirus Evolution. Journal of Molecular Biology, 437, 169512.

  4. Hatfield,B.M., Weidmann,C.A., McCutchin,C.A., Irving,P.S., Nelson,I.M., Felder,S. and Weeks,K.M. (2025) Functional Proximity across an mRNA. Biochemistry, 64, 3854–3865.

  5. Waldern,J.M., Taylor,C., Giannetti,C.A., Irving,P.S., Allen,S.R., Zhu,M., Backofen,R., Mathews,D.H., Weeks,K.M. and Laederach,A. (2025) Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP. Nucleic Acids Res, 53, gkaf433.

  6. Veenbaas,S.D., Koehn,J.T., Irving,P.S., Lama,N.N. and Weeks,K.M. (2025) Ligand-binding pockets in RNA and where to find them. Proceedings of the National Academy of Sciences, 122, e2422346122.

  7. Wang,J. (2025) Genome-Wide Analysis of Stable RNA Secondary Structures across Multiple Organisms Using Chemical Probing Data: Insights into Short Structural Motifs and RNA-Targeting Therapeutics. Biochemistry, 64, 1817–1827.

  8. Kim,J.Y., Furney,A., Benner,B. and Sengupta,A. (2025) Stress-induced changes in endogenous TP53 mRNA 5′ regulatory region. Journal of Biological Chemistry, 301.

  9. Dey,A., Yan,S., Schlick,T. and Laederach,A. (2024) Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses. RNA, 30, 1437–1450.

  10. Tan,A.C., Irving,P.S., Koehn,J.T., Jin,S., Qiu,D.Y. and Weeks,K.M. (2024) Fingerprinting Tertiary Structure in Complex RNAs Using Single-Molecule Correlated Chemical Probing. Biochemistry, 63, 2648–2657.

  11. Dey,A. (2023) Structural Modifications and Novel Protein-Binding Sites in Pre-miR-675—Explaining Its Regulatory Mechanism in Carcinogenesis. Non-Coding RNA, 9, 45.